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SYPL1 synaptophysin like 1 [ Homo sapiens (human) ]

Gene ID: 6856, updated on 2-Nov-2024

Summary

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Official Symbol
SYPL1provided by HGNC
Official Full Name
synaptophysin like 1provided by HGNC
Primary source
HGNC:HGNC:11507
See related
Ensembl:ENSG00000008282 MIM:616665; AllianceGenome:HGNC:11507
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SYPL; H-SP1
Summary
Predicted to be involved in chemical synaptic transmission. Located in extracellular exosome. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 63.3), esophagus (RPKM 56.9) and 25 other tissues See more
Orthologs
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Genomic context

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See SYPL1 in Genome Data Viewer
Location:
7q22.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (106090505..106112576, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (107405910..107427970, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (105730951..105753022, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ataxin 7 like 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:105470396-105471595 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105477786-105478643 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105478644-105479500 Neighboring gene ribosomal protein L13a pseudogene 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105494345-105495094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18524 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:105525198-105525381 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:105528806-105529002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105596161-105596662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105596663-105597162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105602263-105603214 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105603215-105604166 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105631053-105631700 Neighboring gene uncharacterized LOC107986833 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18525 Neighboring gene cadherin related family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105671382-105671882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105683076-105683576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105698686-105699237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26482 Neighboring gene Sharpr-MPRA regulatory region 14293 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105720431-105720970 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105720971-105721508 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105751988-105752820 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18529 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26483 Neighboring gene DDB1 and CUL4 associated factor 13 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18531 Neighboring gene NANOG hESC enhancer GRCh37_chr7:105821183-105821690 Neighboring gene RNA, U6 small nuclear 392, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Molecular cloning of a cDNA encoding a novel protein related to the neuronal vesicle protein synaptophysin. Zhong CZ, et al. Biochim Biophys Acta, 1992 Jan 6. PMID 1730063
  2. Elevated synaptophysin I in the prefrontal cortex of human chronic alcoholics. Henriksson R, et al. Synapse, 2008 Nov. PMID 18720419, Free PMC Article
  3. Pantophysin is a phosphoprotein component of adipocyte transport vesicles and associates with GLUT4-containing vesicles. Brooks CC, et al. J Biol Chem, 2000 Jan 21. PMID 10636906
  4. Evaluation of fecal SYPL1 as a diagnostic biomarker in colorectal cancer. Shu T, et al. Clin Biochem, 2022 May. PMID 35218739
  5. SYPL1 overexpression predicts poor prognosis of hepatocellular carcinoma and associates with epithelial-mesenchymal transition. Chen DH, et al. Oncol Rep, 2017 Sep. PMID 28731154

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Evaluation of fecal SYPL1 as a diagnostic biomarker in colorectal cancer.
    Title: Evaluation of fecal SYPL1 as a diagnostic biomarker in colorectal cancer.
  2. Serum SYPL1 is a promising diagnostic biomarker for colorectal cancer.
    Title: Serum SYPL1 is a promising diagnostic biomarker for colorectal cancer.
  3. SYPL1 overexpression predicts poor prognosis of HCC.
    Title: SYPL1 overexpression predicts poor prognosis of hepatocellular carcinoma and associates with epithelial-mesenchymal transition.
  4. A role is found for synaptophysin I in the enduring neuroplasticity in the prefrontal cortical glutamate circuitry that is associated with ethanol dependence.
    Title: Elevated synaptophysin I in the prefrontal cortex of human chronic alcoholics.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ46439

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chemical synaptic transmission TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in melanosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in secretory granule IEA
Inferred from Electronic Annotation
more info
  
is_active_in synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
synaptophysin-like protein 1
Names
pantophysin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001381910.1 → NP_001368839.1  synaptophysin-like protein 1 isoform c

    Status: VALIDATED

    Source sequence(s)
    AC005095
    Consensus CDS
    CCDS94175.1
    UniProtKB/TrEMBL
    A0A994J846, A8K865
    Related
    ENSP00000516340.1, ENST00000706299.1
    Conserved Domains (1) summary
    pfam01284
    Location:135 → 257
    MARVEL; Membrane-associating domain

  2. NM_001381911.1 → NP_001368840.1  synaptophysin-like protein 1 isoform d

    Status: VALIDATED

    Source sequence(s)
    AC005095
    UniProtKB/TrEMBL
    A8K865
    Conserved Domains (1) summary
    pfam01284
    Location:117 → 239
    MARVEL; Membrane-associating domain

  3. NM_001381912.1 → NP_001368841.1  synaptophysin-like protein 1 isoform e precursor

    Status: VALIDATED

    Source sequence(s)
    AC005095
    UniProtKB/TrEMBL
    A8K865
    Conserved Domains (1) summary
    pfam01284
    Location:87 → 209
    MARVEL; Membrane-associating domain

  4. NM_001381913.1 → NP_001368842.1  synaptophysin-like protein 1 isoform f

    Status: VALIDATED

    Source sequence(s)
    AC005095
    Conserved Domains (2) summary
    pfam01284
    Location:109 → 186
    MARVEL; Membrane-associating domain
    pfam03896
    Location:67 → 148
    TRAP_alpha; Translocon-associated protein (TRAP), alpha subunit

  5. NM_001381915.1 → NP_001368844.1  synaptophysin-like protein 1 isoform g

    Status: VALIDATED

    Source sequence(s)
    AC005095
    Conserved Domains (1) summary
    pfam01284
    Location:24 → 102
    MARVEL; Membrane-associating domain

  6. NM_001381916.1 → NP_001368845.1  synaptophysin-like protein 1 isoform h

    Status: VALIDATED

    Source sequence(s)
    AC005095

  7. NM_001381917.1 → NP_001368846.1  synaptophysin-like protein 1 isoform i precursor

    Status: VALIDATED

    Source sequence(s)
    AC005095
    Conserved Domains (1) summary
    pfam01284
    Location:1 → 81
    MARVEL; Membrane-associating domain

  8. NM_001381918.1 → NP_001368847.1  synaptophysin-like protein 1 isoform j

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10), as well as variant 11, encodes isoform j.
    Source sequence(s)
    AC005095
    Consensus CDS
    CCDS94174.1
    UniProtKB/TrEMBL
    A0A994J5J4, A8K865

  9. NM_001381919.1 → NP_001368848.1  synaptophysin-like protein 1 isoform j

    Status: VALIDATED

    Description
    Transcript Variant: This variant (11), as well as variant 10, encodes isoform j.
    Source sequence(s)
    AC005095
    Consensus CDS
    CCDS94174.1
    UniProtKB/TrEMBL
    A0A994J5J4, A8K865
    Related
    ENSP00000516339.1, ENST00000706298.1

  10. NM_001381920.1 → NP_001368849.1  synaptophysin-like protein 1 isoform k

    Status: VALIDATED

    Description
    Transcript Variant: This variant (12), as well as variant 13, encodes isoform k.
    Source sequence(s)
    AC005095
    Consensus CDS
    CCDS94173.1
    UniProtKB/TrEMBL
    C9JYN0
    Conserved Domains (1) summary
    pfam01284
    Location:91 → 185
    MARVEL; Membrane-associating domain

  11. NM_001381921.1 → NP_001368850.1  synaptophysin-like protein 1 isoform k

    Status: VALIDATED

    Description
    Transcript Variant: This variant (13), as well as variant 12, encodes isoform k.
    Source sequence(s)
    AC005095
    Consensus CDS
    CCDS94173.1
    UniProtKB/TrEMBL
    C9JYN0
    Related
    ENSP00000419070.1, ENST00000470347.1
    Conserved Domains (1) summary
    pfam01284
    Location:91 → 185
    MARVEL; Membrane-associating domain

  12. NM_006754.5 → NP_006745.1  synaptophysin-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_006745.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AC005095
    Consensus CDS
    CCDS5736.1
    UniProtKB/Swiss-Prot
    A4D0R2, Q16563, Q96AR8
    UniProtKB/TrEMBL
    A4D0R1, A8K865
    Related
    ENSP00000011473.2, ENST00000011473.6
    Conserved Domains (1) summary
    pfam01284
    Location:109 → 231
    MARVEL; Membrane-associating domain

  13. NM_182715.4 → NP_874384.1  synaptophysin-like protein 1 isoform b

    See identical proteins and their annotated locations for NP_874384.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AC005095
    Consensus CDS
    CCDS47685.1
    UniProtKB/TrEMBL
    A8K865
    Related
    ENSP00000388336.2, ENST00000455385.7
    Conserved Domains (1) summary
    pfam01284
    Location:86 → 213
    MARVEL; Membrane-associating domain

RNA

  1. NR_167729.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC005095
    Related
    ENST00000706297.1

  2. NR_167730.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC005095

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    106090505..106112576 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    107405910..107427970 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q16563.1 GenPept UniProtKB/Swiss-Prot:Q16563

Gene LinkOut

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